FBI spokesman Chris Murray in Washington declined to comment on the search, and no details of what the agents were looking for could be learned.
After the apartment was searched June 25 and Aug. 1, Hatfill, a 48-year-old physician and bioterrorism expert, denied that he had had anything to do with the attacks and said that the FBI's scrutiny has wrecked his career.
He was recently fired from a $150,000-a-year job at Louisiana State University, where he trained emergency personnel to handle bioterrorism incidents. The dismissal followed an order from the Department of Justice that Hatfill should not be allowed to work on any LSU programs funded by the department.
The FBI's return to the Frederick apartment indicates that despite Hatfill's protests, investigators have not ruled him out as a suspect in the anonymous mailings, which killed five people and disrupted the mail system and the federal government for weeks last fall.
But it is unclear what they hoped to discover that did not turn up in the two previous daylong searches, in which a computer and bags of belongings were removed for inspection.
Pat Clawson, a friend of Hatfill's who is acting as his spokesman, said Hatfill and his attorney, Victor M. Glasberg, had not been informed of the search.
Clawson said Hatfill moved out of the apartment a month ago.
"Why do they have to search a third time?" Clawson said. "Isn't the FBI competent enough to get the job done the first two tries?"
Clawson said that in Hatfill's continuing effort to clear himself, he voluntarily visited the FBI's Washington field office two weeks ago to give a blood sample and leave palm prints and fingerprints. He also offered to give a handwriting sample, but agents said they had obtained some during the searches.
Hatfill's blood sample could be checked for antibodies to anthrax, indicating whether he has recently been exposed to the bacteria. But because Hatfill's work at Fort Detrick required an anthrax vaccine that would have produced antibodies, some scientists say a blood test is not likely to prove anything.
Hatfill's DNA and fingerprints could also be compared with any recovered from the anthrax letters. But officials have said that neither DNA nor fingerprints were found on the envelopes, which had preprinted postage rather than stamps that might bear traces of saliva.
The addresses on the envelopes and the notes inside were handwritten, so handwriting analysts could compare them to Hatfill's writing.